Fifth, we estimate the variance of S(x) using a block jackknife with k = 100 blocks of contiguous SNPs, resulting in minimal non-independence between blocks. Blocks are chosen to include the same number of SNPs, and the jackknife variance is: (8)σS(x)2=101∑j=1100(Sj(x)−Savg(x))2 where Sj(x) is the test statistic computed on blocks 1,…,j − 1, j + 1,…100 and Savg(x) is the mean of the jackknife estimates. We compute an approximate likelihood, L(S∣gcp = x), by assuming (1) that L(S∣gcp = x) = L(S(x)∣gcp = x) and (2) that if gcp = x then S(x)/σS(x) follows a T distribution with 98 degrees of freedom.
